[gmx-users] using nopbc is not equal to using pbc with big box dimensions

[Mark Abraham]

Your use of PME invalidates the comparison.

Mark
On Dec 3, 2013 2:22 AM, "Golshan Hejazi" <golshan.hejazi at yahoo.com> wrote:

> Thanks for your reply. The result is surprisingly different:
>
> with nopbc            Potential energy=       -2.53730634908684e+05
> with large box        Potential energy=  -2.21066633251456e+05
>
> I have tried with very large boxes too! but results are not even similar.
> This is what I am using as input in mdp file:
> pbc                        = no
> nstlist                     = 0
> epsilon_r                = 1.
> ns_type                  = Simple
> coulombtype          = Cut-off
> vdwtype                 = Cut-off
> fourierspacing        = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order             = 4
> ewald_rtol              = 1e-05
> epsilon_surface      = 0
> optimize_fft            = yes
> rlist                        = 0.
> rcoulomb               = 0.
> rvdw                      = 0.
> emtol                     = 1.0
>
> And this is for when I use the large box:
> pbc                       = xyz
> nstlist                   = 10
> epsilon_r              = 1.
> ns_type                = grid
> coulombtype         = pme
> vdwtype                  = Cut-off
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 4
> ewald_rtol               = 1e-05
> epsilon_surface          = 0
> optimize_fft             = yes
> rlist                         = 0.7
> rcoulomb                 = 0.7
> rvdw                       = 0.7
> emtol                     = 1.0
>
>
>
>
> On Monday, December 2, 2013 7:45 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
> wrote:
>
> The fact that images are separated by a distance exceeding the cutoff,
> does not mean that they do not interact electrostatically.
>
> I hope the results are not much different...
>
>
> Dr. Vitaly V. Chaban
>
>
> >
> > On Mon, Dec 2, 2013 at 11:46 PM, Golshan Hejazi <
> golshan.hejazi at yahoo.com>wrote:
> >
> >> Hello,
> >>
> >> I would like to compute the energy of a system in vacuum. For this I
> first
> >> computed energy by using nopbc and putting rculomb=rvdw=0 ...
> >> Then I computed the energy using pbc with a big box dimension (periodic
> >> images are separated by a length more than cutoff )... this means that
> >> periodic images dont interact ... results are different ... but which
> one
> >> is correct?
> >>
> >>
> >> Can you help me to understand this better
> >> G.
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